"Cliquely" is tool that enables the exploration of the co-occurrence patterns of proteins across a wide range of 4,742 fully sequenced genomes from the three domains of life. The data underneath Cliquely covers more than 23 million proteins divided into 404,947 orthologous clusters.
Based on an entry protein of interest, the data set is used to construct a co-occurrence graph based on phylogenetic profiles, with edge weights representing co-occurrence probabilities. Users can direct Cliquely to work with the entire underlying data set, or specifically in the context of Bacteria, Archaea, or Eukaryota. The Bron–Kerbosch algorithm is then used in order to detect maximal cliques in this graph, i.e. fully-connected subgraphs representing meaningful biological networks from different functional categories. Cliquely's results shed light on functional relationships between proteins and protein families, in the context of different levels of taxonomic resolution and with unprecedented underlying data set.
Cliquely can be downloaded from the following website, as a ready-to-run executable. The software is compatible to Windows, and was tested on Windows 10 and Windows 11 machines.
Follow these steps:
- Download the Cliquely zip file of the current version from https://github.com/Cliquely/Cliquely ( at https://github.com/Cliquely/Cliquely/releases ). Unzip it on your own machine. Note that this file contains the user manual of Cliquely.
- Make sure that you place the Cliquely folder where you wish to run it. Note that csv output files will also be placed in this folder.
- To start using Cliquely, simply click the executable, and specify the entry sequence and parameters.
The input of Cliquely includes an entry sequence of interest in Fasta format. The entry sequence is used to search for cliques on a co-occurrence graph, and should be copied to the first text box in the main screen of the software.
Four additional parameters and options below the main text box that users can use in order to refine their investigation:
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Probability: probability of co-occurrence (Pco) for pairs of proteins in the cliques to be found in the same organism.
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Max Clique Size: maximal size for the identified cliques. This parameter allows users to limit run-time for runs that turn out to be too promiscuous - and may lead to results that are not of biological interest.
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Max Cliques: in a similar way to Max Clique Size, this parameter can be used to control promiscuous runs.
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Search in: this selection menu allows users to choose between running their entry protein vs. the entire underlying orthology data set that Cliquey uses, or focus either on Archaea, Bacteria or Eukaryota.
The parameter which controls the very definition of similarity within the reported co-occurrence cliques is Probability, the specified co-occurrence probability threshold (Pco). Cliquey also utilizes this threshold to make the algorithm more efficient, pruning the full co-occurrence graph accordingly. Nodes and edges that are of no relevance to the entry (input) protein are removed, and edges with weights that are smaller than the chosen threshold (Pco) are also removed.
A description of the algorithm pipeline, from input entry to the desired output is provided in the following figure:
Following download and unzipping, users can execute Cliquely by double clicking the exe file. The following screen captures illustrate the process from the user's angle:
- Main screen as you enter the program. The user is asked to enter choices - entry sequence, Probability (Pco, in the range 0-1), Max clique size, Max cliques, dropdown menu for the "Search in" option. The program's defaults is Pco =0.7, this will perform well in in most cases, but users are encouraged to run Cliquely for a range of Pco values, and choose the best Pco for their purposes.
- After you have filled all of the required fields you may click on "Search cliques" and the program will start to calculate the cliques of the entered FASTA sequence, this process may take a few minute.
- When the program finished calculating the cliques of the protein it will show the results within Cliquely's window.
- Cliquely also exports the results to a csv file, and it may be easier to view the results by opening this file, located in the executable folder.
The output is provided as a table of cliques, and can be viewed either in the program's screen or using the csv output file. This table contains the following:
Rows:
Each row in the output table is a clique.
Columns:
- Gene - The query gene that was entered by the user. If the entry sequence was not 100% matched to our cluster representatives, the Gene may be one of BlastP matches.
- Probability - The Pco value provided by the user.
- Incidence - The number of organisms within the "Search in" choice of the user that support the clique.
- Count - The number of proteins in the clique.
- The columns that follow after "Count" detail the members of the clique.
Example for the relationship of the proteins across a universe of 10 Bacterial organisms. The table indicates which organisms contain which proteins. For Example, Protein1 is part of the genome of Bacteria1, but is not part of the genome of Bacteria10.
| Protein1 | Protein2 | |
|---|---|---|
| Bacteria1 | X | |
| Bacteria2 | X | X |
| Bacteria3 | X | X |
| Bacteria4 | X | |
| Bacteria5 | X | X |
| Bacteria6 | X | |
| Bacteria7 | X | X |
| Bacteria8 | X | |
| Bacteria9 | X | X |
| Bacteria10 | X |
Out of the 8 times Protein2 is present, in 5 times Protein1 is also present; Out of the 7 times Protein1 is present, in 5 times Protein1 is also present, thus
In the in the same way
Pco is calculated as the probability of Protein1 to be present in an
organism given that Protein2 is present, multiplied by probability of
Protein2 to be present in an organism given that Protein1 is present:
Notably, in our analysis of orthology Protein1 and Protein2 are in fact representatives of a cluster of orthologs. Thus, the co-occurrence that is estimated using by Cliquely using Pco is the co-occurrence of representatives of different orthology groups.